TSMS-PC-006
Peptide Molecular Weight and Mass Calculation Study Guide
School of Peptide Chemistry · Peptide Chemistry Foundations · Intermediate
Open full lessonLearning objectives
- Explain how peptide mass is derived from amino-acid residues.
- Distinguish average mass from monoisotopic mass.
- Account for terminal groups and covalent modifications.
- Explain how disulfide formation changes calculated mass.
- Recognize why observed LC-MS values may differ from nominal molecular weight.
Executive summary
Peptide molecular weight is calculated from the exact covalent composition of the molecule. A peptide is not simply the sum of free amino-acid molecular weights because each peptide bond forms with formal loss of water. The final calculation must also account for terminal groups, disulfides, labels, conjugates, protecting groups, counterions, and other modifications.
Two mass conventions are commonly used. **Average mass** reflects the weighted natural abundance of isotopes. **Monoisotopic mass** uses the exact mass of the most abundant isotope of each element. Mass spectrometric interpretation requires knowing which convention is being used.
Two mass conventions are commonly used. **Average mass** reflects the weighted natural abundance of isotopes. **Monoisotopic mass** uses the exact mass of the most abundant isotope of each element. Mass spectrometric interpretation requires knowing which convention is being used.
Key takeaways
- Peptide mass depends on exact covalent composition.
- Average and monoisotopic mass serve different purposes.
- Terminal groups and modifications must be included.
- Disulfide formation removes two hydrogens per bond.
- LC-MS reports m/z, not always neutral mass directly.
- Correct mass is strong evidence but not complete identity proof.
Self-review questions
- Why does an n-residue peptide contain n−1 peptide bonds?
- What is the difference between average and monoisotopic mass?
- How does one disulfide bond affect mass?
- Why can sodium adducts appear in a mass spectrum?
- Why is correct intact mass not complete proof of identity?
Use the full lesson to verify your answers.